[factor] orffinder-to-sequence tool

src/cline_tools/gene.fasta

@@ -0,0 +1,238 @@
+>NC_001643.1 Pan troglodytes mitochondrion, complete genome
+GTTTATGTAGCTTACCCCCTCAAAGCAATACACTGAAAATGTTTCGACGGGTTTACATCACCCCATAAAC
+AAACAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGCCCCGTG
+AGTCACCCTCTAAATCGCCATGATCAAAAGGAACAAGTATCAAGCACGCAGCAATGCAGCTCAAAACGCT
+TAGCCTAGCCACACCCCCACGGGAGACAGCAGTGATAAACCTTTAGCAATAAACGAAAGTTTAACTAAGC
+CATACTAACCTCAGGGTTGGTCAATTTCGTGCTAGCCACCGCGGTCATACGATTAACCCAAGTCAATAGA
+AACCGGCGTAAAGAGTGTTTTAGATCACCCCCCCATAAAGCTAAAATTCACCTGAGTTGTAAAAAACTCC
+AGCTGATACAAAATAAACTACGAAAGTGGCTTTAACACATCTGAATACACAATAGCTAAGACCCAAACTG
+GGATTAGATACCCCACTATGCTTAGCCCTAAACTTCAACAGTTAAATTAACAAAACTGCTCGCCAGAACA
+CTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGGAGCCTGTTCTGT
+AATCGATAAACCCCGATCAACCTCACCGCCTCTTGCTCAGCCTATATACCGCCATCTTCAGCAAACCCTG
+ATGAAGGTTACAAAGTAAGCACAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCTATGAGGTGGC
+AAGAAATGGGCTACATTTTCTACCCCAGAAAATTACGATAACCCTTATGAAACCTAAGGGTCAAAGGTGG
+ATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCA
+CCCTCCTCAAGTATACTTCAAAGGATACTTAACTTAAACCCCCTACGTATTTATATAGAGGAGATAAGTC
+GTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACATAAAGCACCCAAC
+TTACACTTAGGAGATTTCAACTCAACTTGACCACTCTGAGCCAAACCTAGCCCCAAACCCCCTCCACCCT
+ACTACCAAACAACCTTAACCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGTAAACCGGCGC
+AATAGACATAGTACCGCAAGGGAAAGATGAAAAATTATACCCAAGCATAATACAGCAAGGACTAACCCCT
+GTACCTTTTGCATAATGAATTAACTAGAAATAACTTTGCAAAGAGAACCAAAGCTAAGACCCCCGAAACC
+AGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTATAG
+GTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTAA
+ATTTACCTACAGAACCCTCTAAATCCCCTTGTAAACTTAACTGTTAGTCCAAAGAGGAACAGCTCTTTAG
+ACACTAGGAAAAAACCTTGTAAAGAGAGTAAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCA
+ATTAAGAAAGCGTTCAAGCTCAACACCCACAACCTTAAAGATCCCAAACATACAACCGAACTCCTTACAC
+CCAATTGGACCAATCTATTACCCCATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTC
+CGCATAAGCCTACATCAGACCAAAATATTAAACTGACAATTAACAGCCTAATATCTACAATCAACCAACA
+AGCCATTATTACCCCCGCTGTTAACCCAACACAGGCATGCCCACAAGGAAAGGTTAAAAAAAGTAAAAGG
+AACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGCATTACCAGTATTAGAGGCACC
+GCCTGCCCGGTGACATATGTTTAACGGCCGCGGTACCCTAACCGTGCAAAGGTAGCATAATCACTTGTTC
+CTTAAATAGGGACTTGTATGAATGGCTCCACGAGGGTTTAGCTGTCTCTTACTTTCAACCAGTGAAATTG
+ACCTACCCGTGAAGAGGCGGGCATAACATAACAAGACGAGAAGACCCTATGGAGCTTTAATTCATTAATG
+CAAACAATACTTAACAAACCTACAGGTCCTAAACTATTAAACCTGCATTAAAAATTTCGGTTGGGGCGAC
+CTCGGAGCACAACCCAACCTCCGAGCAATACATGCTAAGACCTCACCAGTCAAAGCGAATTACTACATCC
+AATTGATCCAATGACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCTATTCCAGAGTC
+CATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAG
+GTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTA
+TCTGTTCTAAATTTCTCCCTGTACGAAAGGACAAGAGAAATGAGGCCTACTTCACAAAGCGCCTTCCCCA
+ATAAATGATATTATCTCAATTTAGCGCCATGCCAACACCCACTCAAGAACAGAGTTTGTTAAGATGGCAG
+AGCCCGGTAATTGCATAAAACTTAAAACTTTACAATCAGAGGTTCAATTCCTCTTCTTGACAACACACCC
+ATGACCAACCTCCTACTCCTCATTGTACCCATCCTAATCGCAATAGCATTCCTAATGCTAACCGAACGAA
+AAATTCTAGGCTACATACAACTACGCAAAGGTCCCAACATTGTAGGTCCTTACGGGCTATTACAGCCCTT
+CGCTGACGCCATAAAACTCTTCACTAAAGAACCCTTAAAACCCTCCACTTCAACCATTACCCTCTACATC
+ACCGCCCCAACCCTAGCCCTCACCATTGCCCTCTTACTATGAACCCCCCTCCCCATACCCAACCCCCTAG
+TCAATCTTAACTTAGGCCTCCTATTTATTCTAGCCACCTCCAGCCTAGCCGTTTACTCAATCCTCTGATC
+AGGGTGAGCATCAAACTCGAACTACGCCTTAATCGGTGCACTACGAGCAGTAGCCCAAACAATCTCATAC
+GAAGTCACTCTAGCCATTATCCTACTGTCAACGCTACTAATAAGTGGCTCCTTCAATCTCTCTACCCTTG
+TCACAACACAAGAGCACCTCTGACTAATCCTGCCAACATGACCCCTGGCCATAATATGATTTATCTCTAC
+ACTAGCAGAGACCAACCGAACTCCCTTCGACCTTACTGAAGGAGAATCTGAACTAGTCTCAGGCTTTAAT
+ATCGAGTATGCCGCAGGCCCCTTTGCCCTATTTTTCATAGCCGAATACATAAACATTATTATAATAAACA
+CCCTCACTGCTACAATCTTCCTAGGAGCAACATACAATACTCACTCCCCTGAACTCTACACGACATATTT
+TGTCACCAAAGCTCTACTTCTAACCTCCCTGTTCCTATGAATTCGAACAGCATATCCCCGATTTCGCTAC
+GACCAGCTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTAGCATCACTCATGTGATATATCT
+CCATACCCACTACAATCTCCAGCATCCCCCCTCAAACCTAAGAAATATGTCTGATAAAAGAATTACTTTG
+ATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTAGGACTATAAGAATCGAACTCATCCCTGAGAA
+TCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAAGTAAGGTCAGCTAAATAAGCTATCGGGCCC
+ATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAATTAATCCCCTAGCCCAACCCATCATCTACTCT
+ACCATCCTTACAGGCACGCTCATTACAGCGCTAAGCTCACACTGATTTTTCACCTGAGTAGGCCTAGAAA
+TAAATATACTAGCTTTTATCCCAATCCTAACCAAAAAAATAAGCCCCCGCTCCACAGAAGCCGCCATCAA
+ATACTTTCTCACACAAGCAACTGCGTCCATAATTCTCCTGATAGCTATCCTCTCCAACAGCATACTCTCC
+GGACAATGAACCATAACCAATACTACCAATCAATACTCATCATTAATAATTATAATAGCAATGGCAATAA
+AACTAGGAATAGCCCCCTTTCACTTTTGAGTTCCAGAAGTTACCCAAGGCACCCCCCTAATATCCGGCCT
+ACTCCTCCTCACATGACAAAAATTAGCCCCTATTTCAATTATATACCAAATCTCCTCATCACTGAACGTA
+AACCTTCTCCTCACCCTTTCAATCTTGTCCATTATAGCAGGCAGCTGAGGCGGACTAAACCAAACCCAAC
+TACGCAAAATCCTAGCATACTCCTCAATCACCCACATAGGCTGAATAATAGCAGTCCTACCATATAACCC
+TAACATAACCATTCTTAATTTAACCATTTACATCATCCTAACTACTACCGCATTTCTGCTACTCAACTTA
+AACTCCAGCACCACAACCCTACTACTATCTCGCACCTGAAACAAGCTAACATGATTAACTCCCCTAATTC
+CATCCACCCTCCTCTCCCTAGGAGGCCTACCCCCACTAACTGGCTTCTTACCCAAATGAGTTATCATCGA
+AGAATTCACAAAAAATAATAGCCTCATCATCCCCACCATCATAGCCATCATCACTCTCCTTAACCTCTAT
+TTCTACCTACGCCTAATCTACTCCACCTCAATTACACTACTTCCCATATCTAATAACGTAAAAATAAAAT
+GACAATTCGAACATACAAAACCCACCCCCTTCCTCCCTACACTCATCACCCTTACCACACTGCTTCTACC
+CATCTCCCCCTTCATACTAATAATCTTATAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCC
+TCAGCAAGTTACAATACTTAATTTCTGCAACAACTAAGGACTGCAAAACCCCACTCTGCATCAACTGAAC
+GCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGATTAATGGGACTTAAACCCACAAACATTTAGT
+TAACAGCTAAACACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCAAGAAAAAAAGGCGGGAGAA
+GCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACCTCAGAGCTGGTAAA
+AAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACCCCACCCTACTG
+ATGTTCACCGACCGCTGACTATTCTCTACAAACCACAAAGATATTGGAACACTATACCTACTATTCGGTG
+CATGAGCTGGAGTCCTGGGCACAGCCCTAAGTCTCCTTATTCGGGCTGAACTAGGCCAACCAGGCAACCT
+CCTAGGTAATGACCACATCTACAATGTCATCGTCACAGCCCATGCATTCGTAATAATCTTCTTCATAGTA
+ATGCCTATTATAATCGGAGGCTTTGGCAACTGGCTAGTTCCCTTGATAATTGGTGCCCCCGACATGGCAT
+TCCCCCGCATAAACAACATAAGCTTCTGGCTCCTGCCCCCTTCTCTCCTACTTCTACTTGCATCTGCCAT
+AGTAGAAGCCGGCGCGGGAACAGGTTGAACAGTCTACCCTCCCTTAGCGGGAAACTACTCGCATCCTGGA
+GCCTCCGTAGACCTAACCATCTTCTCCTTACATCTGGCAGGCATCTCCTCTATCCTAGGAGCCATTAACT
+TCATCACAACAATTATTAATATAAAACCTCCTGCCATGACCCAATACCAAACACCCCTCTTCGTCTGATC
+CGTCCTAATCACAGCAGTCTTACTTCTCCTATCCCTCCCAGTCCTAGCTGCTGGCATCACCATACTATTG
+ACAGATCGTAACCTCAACACTACCTTCTTCGACCCAGCCGGGGGAGGAGACCCTATTCTATATCAACACT
+TATTCTGATTTTTTGGCCACCCCGAAGTTTATATTCTTATCCTACCAGGCTTCGGAATAATTTCCCACAT
+TGTAACTTATTACTCCGGAAAAAAAGAACCATTTGGATATATAGGCATGGTTTGAGCTATAATATCAATT
+GGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGGATAGACGTAGACACCCGAGCCT
+ATTTCACCTCCGCTACCATAATCATTGCTATTCCTACCGGCGTCAAAGTATTCAGCTGACTCGCTACACT
+TCACGGAAGCAATATGAAATGATCTGCCGCAGTACTCTGAGCCCTAGGGTTTATCTTTCTCTTCACCGTA
+GGTGGCCTAACCGGCATTGTACTAGCAAACTCATCATTAGACATCGTGCTACACGACACATACTACGTCG
+TAGCCCACTTCCACTACGTTCTATCAATAGGAGCTGTATTCGCCATCATAGGAGGCTTCATTCACTGATT
+CCCCCTATTCTCAGGCTATACCCTAGACCAAACCTATGCCAAAATCCAATTTGCCATCATGTTCATTGGC
+GTAAACCTAACCTTCTTCCCACAGCACTTCCTTGGCCTATCTGGGATGCCCCGACGTTACTCGGACTACC
+CCGATGCATACACCACATGAAATGTCCTATCATCCGTAGGCTCATTTATCTCCCTGACAGCAGTAATATT
+AATAATTTTCATGATTTGAGAAGCCTTTGCTTCAAAACGAAAAGTCCTAATAGTAGAAGAGCCCTCCGCA
+AACCTGGAATGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTA
+GACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTT
+CAAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTTAACCCCCGTATATCT
+TAATGGCACATGCAGCGCAAGTAGGTCTACAAGATGCTACTTCCCCTATCATAGAAGAACTTATTATCTT
+TCACGACCATGCCCTCATAATTATCTTTCTCATCTGCTTTCTAGTCCTATACGCCCTTTTCCTAACACTC
+ACAACAAAACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAAACCGTCTGAACTATCCTGCCCG
+CCATCATCCTAGTCCTTATTGCCCTACCATCCCTGCGTATCCTTTACATAACAGACGAGGTCAACGACCC
+CTCCTTTACTATTAAATCAATCGGCCATCAATGATATTGAACCTACGAATACACCGACTACGGCGGGCTA
+ATCTTCAACTCCTACATACTCCCCCCATTATTTCTAGAACCAGGTGATCTACGACTCCTTGACGTTGATA
+ACCGAGTGGTCCTCCCAGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATG
+AGCTGTTCCCACATTAGGCCTAAAAACAGACGCAATTCCCGGACGCCTAAACCAAACCACTTTCACCGCC
+ACACGACCAGGAGTATACTACGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCG
+TCCTAGAATTAATCCCTCTAAAAATCTTTGAAATAGGACCCGTATTCACTCTATAGCACCTTCTCTACCC
+CTCTCCAGAGCTCACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACC
+TCTTTACAGTGAAATGCCCCAACTAAATACCGCCGTATGACCCACCATAATTACCCCCATACTCCTGACA
+CTATTTCTCGTCACCCAACTAAAAATATTAAATTCAAATTACCATCTACCCCCCTCACCAAAACCCATAA
+AAATAAAAAACTACAATAAACCCTGAGAACCAAAATGAACGAAAATCTATTCGCTTCATTCGCTGCCCCC
+ACAATCCTAGGCTTACCCGCCGCAGTACTAATCATTCTATTCCCCCCTCTACTGGTCCCCACTTCTAAAC
+ATCTCATCAACAACCGACTAATTACCACCCAACAATGACTAATTCAACTGACCTCAAAACAAATAATAAC
+TATACACAGCACTAAAGGACGAACCTGATCTCTCATACTAGTATCCTTAATCATTTTTATTACCACAACC
+AATCTTCTTGGGCTTCTACCCCACTCATTCACACCAACCACCCAACTATCTATAAACCTAGCCATGGCTA
+TCCCCCTATGAGCAGGCGCAGTAGTCATAGGCTTTCGCTTTAAGACTAAAAATGCCCTAGCCCACTTCTT
+ACCGCAAGGCACACCTACACCCCTTATCCCCATACTAGTTATCATCGAAACTATTAGCCTACTCATTCAA
+CCAATAGCCTTAGCCGTACGTCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAA
+GCGCCACACTAGCATTATCAACTATCAATCTACCCTATGCACTCATTATCTTCACAATTCTAATCCTACT
+GACTATTCTAGAGATCGCCGTCGCCTTAATCCAAGCCTACGTTTTTACACTTCTAGTGAGCCTCTACCTG
+CACGACAACACATAATGACCCACCAATCACATGCCTACCACATAGTAAAACCCAGCCCATGACCCCTAAC
+AGGGGCCCTCTCGGCCCTCCTAATAACCTCCGGCCTGGCCATATGATTCCACTTCTACTCCACAACACTA
+CTCACACTAGGCTTACTAACTAACACATTGACCATATATCAATGATGACGCGATGTTATACGAGAAGGCA
+CATACCAAGGCCACCACACACCACCCGTCCAAAAAGGTCTCCGATATGGGATAATTCTTTTTATTACCTC
+AGAAGTTTTTTTCTTTGCAGGATTTTTTTGAGCTTTCTACCACTCCAGCCTAGCCCCTACCCCCCAGCTA
+GGAGGACACTGGCCCCCAACAGGTATTACCCCACTAAATCCCCTAGAAGTCCCACTCCTAAACACATCTG
+TATTACTCGCATCAGGAGTATCAATTACTTGAGCCCATCACAGCTTAATAGAAAATAACCGAAACCAAAT
+AATTCAAGCACTGCTTATTACGATTCTACTAGGTCTTTATTTTACCCTCCTACAAGCCTCAGAATATTTC
+GAATCCCCTTTTACCATTTCCGATGGCATCTACGGCTCAACATTCTTTGTAGCCACAGGCTTCCACGGAC
+TCCACGTCATTATTGGATCAACTTTCCTCACTATCTGCCTCATCCGCCAACTAATATTTCACTTCACATC
+CAAACATCACTTCGGCTTTCAAGCCGCCGCCTGATACTGACACTTCGTAGATGTAGTCTGACTATTTCTA
+TATGTCTCTATTTACTGATGAGGATCTTACTCTTTTAGTATAAGTAGTACCGTTAACTTCCAATTAACTA
+GTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGTCCTAATTTTAATAACCAATACCCTTCTAGCCCT
+ACTACTGATAATTATCACATTCTGACTACCACAACTCAACAGCTACATAGAAAAATCTACCCCTTACGAA
+TGTGGCTTCGACCCTATATCCCCCGCCCGCGTCCCCTTCTCCATAAAATTTTTCCTAGTAGCCATCACCT
+TCCTATTATTTGACCTAGAAATTGCCCTCCTATTGCCCTTACCTTGAGCCCTACAAACGGCCAACCTACC
+ACTAATAGTCACATCATCCCTCTTATTAATTACTATCCTAGCCCTAAGCCTCGCCTACGAATGATTACAA
+AAAGGGTTAGACTGAACCGAATTGGTATATAGTTTAAATAAAACGAATGATTTCGACTCATTAAATTATG
+ATAATCATATTTACCAAATGCCCCTTATTTATATAAATATTATACTAGCATTTACCATCTCACTTCTAGG
+AATACTAGTATATCGCTCACACCTAATATCTTCCCTACTATGCCTAGAAGGAATAATACTATCACTGTTC
+ATCATAGCCACCCTCATAACCCTCAATACTCACTCCCTCTTAGCCAATATTGTACCCATCACCATACTAG
+TCTTTGCTGCCTGCGAAGCAGCAGTAGGTCTAGCACTACTAGTTTCAATCTCTAACACATATGGCTTAGA
+CTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCATCCCGACAATTATATTACTACCACTAA
+CATGATTCTCTAAAAAACGTATAATTTGAATCAACACAACCACTCACAGCCTAATTATCAGCACCATTCC
+CTTACTATTTTTTAACCAAATTAACAACAACCTATTCAGCTGTTCCCTGCCCTTCTCCTCCGACCCCTTA
+ACAACTCCCCTCCTAATATTAACTGCTTGACTTCTACCCCTCACAATCATAGCAAGCCAGCGCCACCTAT
+CCAACGAACCACTATCACGAAAAAAACTCTACCTCTCCATGCTAATTTCCCTCCAAATCTCCTTAATTAT
+AACATTCTCGGCCACAGAGCTAATTATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCCTGGCT
+ATCATCACCCGATGGGGTAACCAACCAGAACGCCTGAACGCAGGTACATACTTCCTATTCTATACCCTAG
+TAGGCTCCCTCCCCCTACTCATCGCACTAATCTATACCCACAACACCCTAGGCTCACTAAATATCCTATT
+ACTCACTCTTACAACCCAAGAACTATCAAACACCTGAGCCAACAACTTAATATGACTAGCGTACACGATG
+GCTTTCATGGTAAAAATACCCCTTTACGGACTCCACCTATGACTCCCTAAAGCCCATGTCGAAGCCCCTA
+TTGCCGGGTCAATGGTACTTGCTGCAGTACTCTTAAAATTAGGTGGCTATGGCATAATACGCCTCACACT
+CATCCTCAACCCCCTAACAAAACATATAGCCTATCCCTTCCTCATGTTGTCCTTATGAGGTATAATCATA
+ACAAGCTCCATCTGCCTGCGACAAACAGACCTAAAATCGCTCATTGCATACCCTTCAGTCAGCCACATAG
+CCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAATTATCCTCATAATCGC
+CCACGGACTTACATCCTCATTATTATCCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATC
+ATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTGGCAAGCCTCG
+CTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTG
+ATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTT
+ACCACAACACAATGAGGCTCACTCACCCACCACATTAATAGCATAAAGCCCTCATTCACACGAGAAAACA
+CTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCAC
+CTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCACGACCCCTTATT
+TACCGAGAAAGCTTATAAGAACTGCTAACTCGTATTCCCATGCCTAACAACATGGCTTTCTCAACTTTTA
+AAGGATAACAGTTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACC
+ATGTATGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCCATCCTCGGCGCCCTCATTAACC
+CTAACAAAAAAAACTCATACCCCCATTACGTGAAATCCATTATCGCATCCACCTTTATCATTAGCCTTTT
+CCCCACAACAATATTCATATGCCTAGACCAAGAAACTATTATCTCGAACTGACACTGAGCAACAACCCAA
+ACAACCCAACTCTCCCTGAGCTTTAAACTAGACTATTTCTCCATAACATTTATCCCCGTAGCACTGTTCG
+TTACATGATCCATCATAGAATTCTCACTATGATATATAGACTCAGACCCCAACATCAACCAATTCTTCAA
+ATACTTACTTATCTTCCTAATTACTATACTAATCCTAGTCACCGCTAACAACCTATTCCAACTCTTCATC
+GGCTGAGAAGGCGTAGGAATTATATCCTTTCTACTCATTAGCTGATGGTACGCCCGAACAGATGCCAACA
+CAGCAGCCATCCAAGCAATCCTATATAACCGTATCGGTGATATTGGTTTTGTCCTAGCCCTAGCATGATT
+TCTCCTACACTCCAACTCATGAGATCCACAACAAATAATCCTCCTAAGTACTAATACAGACCTTACTCCA
+CTACTAGGCTTCCTCCTAGCAGCAGCAGGCAAATCAGCTCAACTAGGCCTTCACCCCTGACTCCCCTCAG
+CCATAGAAGGCCCTACCCCTGTTTCAGCCCTACTCCACTCAAGCACCATAGTCGTAGCAGGAATCTTCCT
+ACTCATCCGCTTCTACCCCCTAGCAGAGAATAACCCACTAATCCAAACTCTCACGCTATGCCTAGGCGCT
+ATCACCACCCTATTCGCAGCAGTCTGCGCCCTCACACAAAATGACATCAAAAAAATCGTGGCCTTCTCCA
+CTTCAAGCCAACTAGGACTCATAATAGTTACAATCGGTATCAACCAACCACACCTAGCATTCCTTCACAT
+CTGCACCCACGCTTTCTTCAAAGCCATACTATTCATATGCTCCGGATCCATTATTCACAACCTCAATAAT
+GAGCAAGACATTCGAAAAATAGGAGGATTACTCAAAACCATACCCCTCACTTCAACCTCCCTCACCATTG
+GGAGCCTAGCATTAGCAGGAATACCCTTCCTCACAGGTTTCTACTCCAAAGACCTCATCATCGAAACCGC
+TAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGCCACCTCTCTGACAAGCGCCTAC
+AGCACCCGAATAATCCTCCTCACCCTAACAGGTCAACCTCGCTTCCCAACCCTCACCAACATTAACGAAA
+ACAACCCCACTCTGTTAAATCCCATTAAACGCCTAACCATTGGAAGCTTATTTGCAGGATTTCTCATTAC
+CAACAACATTCTCCCCATATCTACTCCCCAAGTGACAATTCCCCTTTACTTAAAACTTACAGCCCTAGGC
+GTTACTTCCCTAGGACTTCTAACAGCCCTAGACCTCAATTACCTAACCAGCAAGCTCAAAATAAAATCCC
+CACTATATACATTTCACTTCTCTAATATACTCGGATTCTACCCTAACATTATACACCGCTCGATCCCCTA
+TCTAGGCCTTCTTACAAGCCAAAACCTACCCCTACTTCTTCTAGACCTGACCTGACTAGAGAAACTATTA
+CCTAAAACAATTTCACAGTACCAAATCTCCGCTTCCATTACCACCTCAACCCAAAAAGGCATGATCAAAC
+TTTATTTCCTCTCTTTTTTCTTCCCTCTCATCTTAACCTTACTCCTAATCACATAACCTATTCCCCCGAG
+CAATCTCAATCACAATGTATACACCAACAAACAATGTCCAACCAGTAACTACTACTAACCAACGCCCATA
+ATCATATAAGGCCCCCGCACCAATAGGATCCTCCCGAATCAGCCCTGGCCCCTCCCCTTCATAAATTATT
+CAACTTCCCACGCTATTAAAATTTACCACAACCACCATCCCATCATACCCTTTTACCCATAACACTAATC
+CTACCTCCATCGCCAGTCCTACTAAAACACTAACCAAAACCTCAACCCCTGACCCCCATGCCTCAGGATA
+CTCCTCAATAGCCATAGCCGTAGTATACCCAAAAACAACCATTATTCCCCCCAAATAAATTAAAAAAACC
+ATTAAACCTATATAACCTCCCCCATAATTCAAAATGATGGCACACCCAACTACACCACTAACAATCAATA
+CTAAACCCCCATAAATGGGAGAAGGCTTAGAAGAAAACCCCACAAACCCTATCACTAAACTCACACTCAA
+TAAAAATAAAGCATATGTCATTATTCTCGCACGGACTACAACCACGACCAATGATATGAAAAACCATCGT
+TGTATTTCAACTACAAGAACACCAATGACCCCGACACGCAAAATTAACCCACTAATAAAATTAATTAATC
+ACTCATTTATCGACCTCCCCACCCCATCCAACATTTCCGCATGATGGAACTTCGGCTCACTTCTCGGCGC
+CTGCCTAATCCTTCAAATTACCACAGGATTATTCCTAGCTATACACTACTCACCAGACGCCTCAACCGCC
+TTCTCGTCGATCGCCCACATCACCCGAGACGTAAACTATGGTTGGATCATCCGCTACCTCCACGCTAACG
+GCGCCTCAATATTTTTTATCTGCCTCTTCCTACACATCGGCCGAGGTCTATATTACGGCTCATTTCTCTA
+CCTAGAAACCTGAAACATTGGCATTATCCTCTTGCTCACAACCATAGCAACAGCCTTTATGGGCTATGTC
+CTCCCATGAGGCCAAATATCCTTCTGAGGAGCCACAGTAATTACAAACCTACTGTCCGCTATCCCATACA
+TCGGAACAGACCTGGTCCAGTGAGTCTGAGGAGGCTACTCAGTAGACAGCCCTACCCTTACACGATTCTT
+CACCTTCCACTTTATCTTACCCTTCATCATCACAGCCCTAACAACACTTCATCTCCTATTCTTACACGAA
+ACAGGATCAAATAACCCCCTAGGAATCACCTCCCACTCCGACAAAATTACCTTCCACCCCTACTACACAA
+TCAAAGATATCCTTGGCTTATTCCTTTTCCTCCTTATCCTAATGACATTAACACTATTCTCACCAGGCCT
+CCTAGGCGATCCAGACAACTATACCCTAGCTAACCCCCTAAACACCCCACCCCACATTAAACCCGAGTGA
+TACTTTCTATTTGCCTACACAATCCTCCGATCCATCCCCAACAAACTAGGAGGCGTCCTCGCCCTACTAC
+TATCTATCCTAATCCTAACAGCAATCCCTGTCCTCCACACATCCAAACAACAAAGCATAATATTTCGCCC
+ACTAAGCCAACTGCTTTACTGACTCCTAGCCACAGACCTCCTCATCCTAACCTGAATCGGAGGACAACCA
+GTAAGCTACCCCTTCATCACCATCGGACAAATAGCATCCGTATTATACTTCACAACAATCCTAATCCTAA
+TACCAATCGCCTCTCTAATCGAAAACAAAATACTTGAATGAACCTGCCCTTGTAGTATAAACTAATACAC
+CGGTCTTGTAAACCGGAAACGAAAACTTTCTTCCAAGGACAAATCAGAGAAAAAGTAATTAACTTCACCA
+TCAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAAATTTAGGTAC
+CACCTAAGTACTGGCTCATTCATTACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATAT
+CGTACAGTACCATATCACCCAACTACCTATAGTACATAAAATCCACTCCCACATCAAAACCTTCACTCCA
+TGCTTACAAGCACGCACAACAATCAACTCCCAACTGTCGAACATAAAACACAATTCCAACGACACCCCTC
+CCCCACCCCGATACCAACAGACCTATCTCCCCTTGACAGAACATAGTACATACAACCATACACCGTACAT
+AGCACATTACAGTCAAACCCCTCCTCGCCCCCACGGATGCTCCCCCTCAGATAGGAATCCCTTGGTCACC
+ATCCTCCGTGAAATCAATATCCCGCACAAGAGTGACTCTCCTCGCTCCGGGCCCATAACATCTGGGGGTA
+GCTAAAGTGAACTGTATCCGACATCTGGTTCCTACCTCAGGGCCATGAAGTTCAAAAGACTCCCACACGT
+TCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCAGTCACGGGAGCCTTCCA
+TGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAAACGCTGGCCCCGGAGCACCCT
+ATGTCGCAGTATCTGTCTTTGATTCCTGCCCCATTGTATTATTTATCGCACCTACGTTCAATATTACGAC
+CTAGCATACCTACTAAAGTGTGTTGATTAATTAATGCTTGCAGGACATAACAACAGCAGCAAAATGCTCA
+CATAACTGCTTTCCACACCAACATCATAACAAAAAATTCCCACAAACCCCCCCTTCCCCCCGGCCACAGC
+ACTCAAACAAATCTCTGCCAAACCCCAAAAACAAAGAACCCAGACGCCAGCCTAGCCAGACTTCAAATTT
+CATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCTCAATTAACATGCCCTCCCCCCTCAACTCCCATT
+CTACTAGCCCCAGCAACGTAACCCCCTACTCACCCTACTCAACACATATACCGCTGCTAACCCCATACCC
+TGAACCAACCAAACCCCAAAGACACCCCTACACA

src/cline_tools/help_pages/orffinder-to-gtf.txt

@@ -0,0 +1,35 @@
+USAGE
+  orffinder-to-gtf [-in input] [-infmt format] [-out output] [-outfmt format] [-orf_size int]
+      [-remove_nested boolean] [-trim_trailing boolean] [-max_orfs_per_sequence int]
+      [-attr_name string]
+
+DESCRIPTION
+      ORFFinder Python v1.5
+
+PARAMETERS
+[-h]
+Shows this interface.
+
+[-in (string)]:
+Input nucleotide sequence to extract ORFs from.
+
+[-infmt (string)]:
+Can be "fasta", "genbank", or any other Biopython supported format. Default: "fasta"
+
+[-out (string)]
+Optional output file. If not specified, will output to stdout.
+
+[-orf_size (integer)]
+Minimum size (in nucleotides) of ORF. Default: 75
+
+[-remove_nested (boolean)]
+Remove ORFs that are completely nested in another ORF. Default: False
+
+[-trim_trailing (boolean)]
+Remove ORFs that have a start codon but no stop codon at the edges of the sequence. Default: False
+
+[-max_orfs_per_sequence (integer)]
+Maximum number of ORFs to return per sequence, sorted by length. Default: -1 (no limit)
+
+[-attr_name (string)]
+Attribute ID name in GTF file. Suffixed by ORF index number. Default: "ORF_"

src/cline_tools/help_pages/orffinder-to-sequence.txt

@@ -0,0 +1,41 @@
+USAGE
+  orffinder-to-gtf [-in input] [-infmt format] [-out output] [-orf_size int]
+      [-remove_nested boolean] [-trim_trailing boolean] [-max_orfs_per_sequence int]
+      [-attr_name string] [-outtype protein/nucleotide]
+
+DESCRIPTION
+      ORFFinder Python v1.5
+
+PARAMETERS
+[-h]
+Shows this interface.
+
+[-in (string)]:
+Input nucleotide sequence to extract ORFs from.
+
+[-infmt (string)]:
+Can be "fasta", "genbank", or any other Biopython supported format. Default: "fasta"
+
+[-out (string)]
+Optional output file. If not specified, will output to stdout.
+
+[-outfmt (string)]:
+Can be "fasta" or "fasta-2line". Default: "fasta"
+
+[-orf_size (integer)]
+Minimum size (in nucleotides) of ORF. Default: 75
+
+[-remove_nested (boolean)]
+Remove ORFs that are completely nested in another ORF. Default: False
+
+[-trim_trailing (boolean)]
+Remove ORFs that have a start codon but no stop codon at the edges of the sequence. Default: False
+
+[-max_orfs_per_sequence (integer)]
+Maximum number of ORFs to return per sequence, sorted by length. Default: -1 (no limit)
+
+[-attr_name (string)]
+Attribute ID name in GTF file. Suffixed by ORF index number. Default: "ORF_"
+
+[-outtype (string)]
+Can be "protein" or "nucleotide". Default: "nucleotide"

src/cline_tools/orffinder-to-gtf.py

@@ -1,8 +1,9 @@
 import sys
+import os
 from Bio import SeqIO
 from orffinder import orffinder
 
-arguments = sys.argv
+arguments = sys.argv + [""]
 classed_arguments = {"orf_size": "75", "max_orfs_per_sequence": "-1", "remove_nested": "False", "trim_trailing": "False", "infmt": "fasta", "attr_name": "ORF_"}
 
 try:
@@ -14,6 +15,11 @@
 
             classed_arguments[argument[1:]] = arguments[i + 1]
 
+    if "h" in classed_arguments.keys():
+        help_output = open("help_pages/orffinder-to-gtf.txt", "r").read()
+        print(help_output)
+        os._exit(1)
+
     sequences = SeqIO.parse(classed_arguments["in"], classed_arguments["infmt"])
 
     orf_size = int(classed_arguments["orf_size"])